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Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis.

Pinard D, Mizrachi E, Hefer CA, Kersting AR, Joubert F, Douglas CJ, Mansfield SD, Myburg AA - BMC Genomics (2015)

Bottom Line: In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production.CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit.The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa. desre.pinard@fabi.up.ac.za.

ABSTRACT

Background: Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink.

Results: Here, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production.

Conclusions: CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.

No MeSH data available.


Total gene expression levels of GT domain families in E. grandis and P. trichocarpa xylem and leaf tissues. (a) Expression level per glycosyl transferase (GT) family in E. grandis in xylem and leaf tissues. The y-axis shows the transcript abundance in FPKM, the x-axis shows the GT family with xylem in brown, and leaf in green. (b) GT domain family (x-axis) expression level for P. trichocarpa xylem and leaf tissues in FPKM (y-axis).
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Fig4: Total gene expression levels of GT domain families in E. grandis and P. trichocarpa xylem and leaf tissues. (a) Expression level per glycosyl transferase (GT) family in E. grandis in xylem and leaf tissues. The y-axis shows the transcript abundance in FPKM, the x-axis shows the GT family with xylem in brown, and leaf in green. (b) GT domain family (x-axis) expression level for P. trichocarpa xylem and leaf tissues in FPKM (y-axis).

Mentions: For the GT family of CAZyme genes, the expression pattern was similar in E. grandis and P. trichocarpa. The majority of GT domain families were expressed at a low level in E. grandis and P. trichocarpa xylem and leaf tissue, which indicates that they are involved in other aspects of carbohydrate metabolism, rather than CW biosynthesis (Figure 4). GT1 family showed higher expression investment in the leaf tissue as opposed to the xylem tissue in both E. grandis and P. trichocarpa. The GT domain families identified in this study as contributing to the majority (80%) of expression investment in the immature xylem compared to the other five tissues in E. grandis (Figure 3, Additional file 9) showed greater expression investment in both E. grandis and P. trichocarpa xylem compared to leaf (Figure 4). These include the domain families that have been implicated in cellulose and hemicellulose biosynthesis, namely GT2, GT4, GT8, GT14, GT31, GT43, and GT47. The conservation of these expression investment patterns between source (mature leaves) and sink (immature xylem) tissues of divergent tree species indicates a conserved mechanism for CW biosynthesis at the functional domain level, and highlights the importance of regulation of these genes at the level of transcript abundance.Figure 4


Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis.

Pinard D, Mizrachi E, Hefer CA, Kersting AR, Joubert F, Douglas CJ, Mansfield SD, Myburg AA - BMC Genomics (2015)

Total gene expression levels of GT domain families in E. grandis and P. trichocarpa xylem and leaf tissues. (a) Expression level per glycosyl transferase (GT) family in E. grandis in xylem and leaf tissues. The y-axis shows the transcript abundance in FPKM, the x-axis shows the GT family with xylem in brown, and leaf in green. (b) GT domain family (x-axis) expression level for P. trichocarpa xylem and leaf tissues in FPKM (y-axis).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4440533&req=5

Fig4: Total gene expression levels of GT domain families in E. grandis and P. trichocarpa xylem and leaf tissues. (a) Expression level per glycosyl transferase (GT) family in E. grandis in xylem and leaf tissues. The y-axis shows the transcript abundance in FPKM, the x-axis shows the GT family with xylem in brown, and leaf in green. (b) GT domain family (x-axis) expression level for P. trichocarpa xylem and leaf tissues in FPKM (y-axis).
Mentions: For the GT family of CAZyme genes, the expression pattern was similar in E. grandis and P. trichocarpa. The majority of GT domain families were expressed at a low level in E. grandis and P. trichocarpa xylem and leaf tissue, which indicates that they are involved in other aspects of carbohydrate metabolism, rather than CW biosynthesis (Figure 4). GT1 family showed higher expression investment in the leaf tissue as opposed to the xylem tissue in both E. grandis and P. trichocarpa. The GT domain families identified in this study as contributing to the majority (80%) of expression investment in the immature xylem compared to the other five tissues in E. grandis (Figure 3, Additional file 9) showed greater expression investment in both E. grandis and P. trichocarpa xylem compared to leaf (Figure 4). These include the domain families that have been implicated in cellulose and hemicellulose biosynthesis, namely GT2, GT4, GT8, GT14, GT31, GT43, and GT47. The conservation of these expression investment patterns between source (mature leaves) and sink (immature xylem) tissues of divergent tree species indicates a conserved mechanism for CW biosynthesis at the functional domain level, and highlights the importance of regulation of these genes at the level of transcript abundance.Figure 4

Bottom Line: In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production.CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit.The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20 Hatfield, Pretoria, 0028, South Africa. desre.pinard@fabi.up.ac.za.

ABSTRACT

Background: Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink.

Results: Here, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production.

Conclusions: CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.

No MeSH data available.